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Introduction to the phylocomr package

Scott Chamberlain and Jeroen Ooms

2024-10-28

Source: vignettes/phylocomr.Rmd
phylocomr.Rmd

phylocomr is an R client for Phylocom - a C library for Analysis of Phylogenetic Community Structure and Character Evolution.

Phylocom home page is at https://phylodiversity.net/phylocom/. The source code for Phylocom is at https://github.com/phylocom/phylocom/.

Phylocom is usually used either on the command line or through the R package picante, which has duplicated some of the Phylocom functionality.

Phylocom has been cited nearly 1000 times according to Google Scholar, so is clearly a very widely used piece of software. The goal with this package is to make it even easier to use - and in particular, to incorporate its use into a reproducible workflow entirely in R instead of going to the shell/command line for Phylocom usage. (Yes, some of Phylocom functionality is in picante, but not all.)

In terms of performance, some functionality will be faster here than in picante, but the maintainers of picante have re-written some Phylocom functionality in C/C++, so performance should be similar in those cases.

Install

Install ape for below examples:

Stable phylocomr version from CRAN

install.packages("phylocomr")

Or, the development version from Github

devtools::install_github("ropensci/phylocomr")

phylomatic 

taxa_file <- system.file("examples/taxa", package = "phylocomr")
phylo_file <- system.file("examples/phylo", package = "phylocomr")
(taxa_str <- readLines(taxa_file))
(phylo_str <- readLines(phylo_file))
ph_phylomatic(taxa = taxa_str, phylo = phylo_str)

aot 

traits_file <- system.file("examples/traits_aot", package = "phylocomr")
phylo_file <- system.file("examples/phylo_aot", package = "phylocomr")
traitsdf_file <- system.file("examples/traits_aot_df", package = "phylocomr")
traits <- read.table(text = readLines(traitsdf_file), header = TRUE,
  stringsAsFactors = FALSE)
phylo_str <- readLines(phylo_file)
ph_aot(traits = traits, phylo = phylo_str)

bladj 

ages_file <- system.file("examples/ages", package = "phylocomr")
phylo_file <- system.file("examples/phylo_bladj", package = "phylocomr")
ages_df <- data.frame(
  a = c('malpighiales','salicaceae','fabaceae','rosales','oleaceae',
        'gentianales','apocynaceae','rubiaceae'),
  b = c(81,20,56,76,47,71,18,56)
)
phylo_str <- readLines(phylo_file)
res <- ph_bladj(ages = ages_df, phylo = phylo_str)

if (requireNamespace("ape")) {
  library(ape)
  plot(read.tree(text = res))
}
plot
plot